orthanc 文件存储服务中使用数据库查询

FilesystemStorage.h

添加声明 class ServerIndex;

/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2022 Osimis S.A., Belgium
 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this program. If not, see
 * <http://www.gnu.org/licenses/>.
 **/


#pragma once

#include "../OrthancFramework.h"

#if !defined(ORTHANC_SANDBOXED)
#  error The macro ORTHANC_SANDBOXED must be defined
#endif

#if ORTHANC_SANDBOXED == 1
#  error The class FilesystemStorage cannot be used in sandboxed environments
#endif

#include "IStorageArea.h"
#include "../Compatibility.h"  // For ORTHANC_OVERRIDE

#include <stdint.h>
#include <boost/filesystem.hpp>
#include <set>







namespace Orthanc
{
    class ServerIndex;
  class ORTHANC_PUBLIC FilesystemStorage : public IStorageArea
  {
    // TODO REMOVE THIS
    friend class FilesystemHttpSender;
    friend class FileStorageAccessor;

  private:
    boost::filesystem::path root_;
    bool                    fsyncOnWrite_;

    boost::filesystem::path GetPath(const std::string& uuid) const;

    void Setup(const std::string& root);
 
    ServerIndex* _index;
   

    
    
#if ORTHANC_BUILDING_FRAMEWORK_LIBRARY == 1
    // Alias for binary compatibility with Orthanc Framework 1.7.2 => don't use it anymore
    explicit FilesystemStorage(std::string root);
#endif

#if ORTHANC_BUILDING_FRAMEWORK_LIBRARY == 1
    // Binary compatibility with Orthanc Framework <= 1.8.2
    void Read(std::string& content,
              const std::string& uuid,
              FileContentType type);
#endif

  public:
    explicit FilesystemStorage(const std::string& root);

    FilesystemStorage(const std::string& root,
                      bool fsyncOnWrite);

    virtual void Create(const std::string& uuid,
                        const void* content, 
                        size_t size,
                        FileContentType type) ORTHANC_OVERRIDE;

    virtual IMemoryBuffer* Read(const std::string& uuid,
                                FileContentType type) ORTHANC_OVERRIDE;

    virtual IMemoryBuffer* ReadRange(const std::string& uuid,
                                     FileContentType type,
                                     uint64_t start /* inclusive */,
                                     uint64_t end /* exclusive */) ORTHANC_OVERRIDE;

    virtual bool HasReadRange() const ORTHANC_OVERRIDE;

    virtual void Remove(const std::string& uuid,
                        FileContentType type) ORTHANC_OVERRIDE;

    virtual void SetDbIndex(ServerIndex* severIndex) ORTHANC_OVERRIDE;

  

    void ListAllFiles(std::set<std::string>& result) const;

    uintmax_t GetSize(const std::string& uuid) const;

    void Clear();

    uintmax_t GetCapacity() const;

    uintmax_t GetAvailableSpace() const;
  };
}

FilesystemStorage.cpp

引入

#include "../../OrthancServer/Sources/ServerIndex.h"

/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2022 Osimis S.A., Belgium
 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this program. If not, see
 * <http://www.gnu.org/licenses/>.
 **/


#include "../PrecompiledHeaders.h"
#include "FilesystemStorage.h"

// http://stackoverflow.com/questions/1576272/storing-large-number-of-files-in-file-system
// http://stackoverflow.com/questions/446358/storing-a-large-number-of-images

#include "../Logging.h"
#include "../OrthancException.h"
#include "../StringMemoryBuffer.h"
#include "../SystemToolbox.h"
#include "../Toolbox.h"

#include <boost/filesystem/fstream.hpp>

#include "../../OrthancServer/Sources/ServerIndex.h"


static std::string ToString(const boost::filesystem::path& p)
{
#if BOOST_HAS_FILESYSTEM_V3 == 1
  return p.filename().string();
#else
  return p.filename();
#endif
}


namespace Orthanc
{
  boost::filesystem::path FilesystemStorage::GetPath(const std::string& uuid) const
  {
    namespace fs = boost::filesystem;
    if (!Toolbox::IsUuid(uuid))
    {
      throw OrthancException(ErrorCode_ParameterOutOfRange);
    }
    std::list<std::string> result;
  _index->GetChildren(result,"bbd94cca-0e327302-856c3822-8b0d3e87-ba3e4fff");
    fs::path path = root_;
    std::time_t const now_c = std::time(0);
    std::stringstream ss;
    ss << std::put_time(std::localtime(&now_c), "%F");

    path /= ss.str();
    path /= std::string(&uuid[0], &uuid[2]);
    path /= std::string(&uuid[2], &uuid[4]);
    path /= uuid;

#if BOOST_HAS_FILESYSTEM_V3 == 1
    path.make_preferred();
#endif

    return path;
  }

  void FilesystemStorage::Setup(const std::string& root)
  {
    //root_ = boost::filesystem::absolute(root).string();
    root_ = root;

    SystemToolbox::MakeDirectory(root);
  }

  FilesystemStorage::FilesystemStorage(const std::string &root) :
    fsyncOnWrite_(false)
  {
    Setup(root);
  }

  FilesystemStorage::FilesystemStorage(const std::string &root,
                                       bool fsyncOnWrite) :
    fsyncOnWrite_(fsyncOnWrite)
  {
    Setup(root);
  }



  static const char* GetDescriptionInternal(FileContentType content)
  {
    // This function is for logging only (internal use), a more
    // fully-featured version is available in ServerEnumerations.cpp
    switch (content)
    {
      case FileContentType_Unknown:
        return "Unknown";

      case FileContentType_Dicom:
        return "DICOM";

      case FileContentType_DicomAsJson:
        return "JSON summary of DICOM";

      case FileContentType_DicomUntilPixelData:
        return "DICOM until pixel data";

      default:
        return "User-defined";
    }
  }


  void FilesystemStorage::Create(const std::string& uuid,
                                 const void* content, 
                                 size_t size,
                                 FileContentType type)
  {
    LOG(INFO) << "Creating attachment \"" << uuid << "\" of \"" << GetDescriptionInternal(type) 
              << "\" type (size: " << (size / (1024 * 1024) + 1) << "MB)";

    boost::filesystem::path path;
    
    path = GetPath(uuid);

    if (boost::filesystem::exists(path))
    {
      // Extremely unlikely case: This Uuid has already been created
      // in the past.
      throw OrthancException(ErrorCode_InternalError);
    }

    if (boost::filesystem::exists(path.parent_path()))
    {
      if (!boost::filesystem::is_directory(path.parent_path()))
      {
        throw OrthancException(ErrorCode_DirectoryOverFile);
      }
    }
    else
    {
      if (!boost::filesystem::create_directories(path.parent_path()))
      {
        throw OrthancException(ErrorCode_FileStorageCannotWrite);
      }
    }

    SystemToolbox::WriteFile(content, size, path.string(), fsyncOnWrite_);
  }


  IMemoryBuffer* FilesystemStorage::Read(const std::string& uuid,
                                         FileContentType type)
  {
    LOG(INFO) << "Reading attachment \"" << uuid << "\" of \"" << GetDescriptionInternal(type) 
              << "\" content type";

    std::string content;
    SystemToolbox::ReadFile(content, GetPath(uuid).string());

    return StringMemoryBuffer::CreateFromSwap(content);
  }


  IMemoryBuffer* FilesystemStorage::ReadRange(const std::string& uuid,
                                              FileContentType type,
                                              uint64_t start /* inclusive */,
                                              uint64_t end /* exclusive */)
  {
    LOG(INFO) << "Reading attachment \"" << uuid << "\" of \"" << GetDescriptionInternal(type) 
              << "\" content type (range from " << start << " to " << end << ")";

    std::string content;
    SystemToolbox::ReadFileRange(
      content, GetPath(uuid).string(), start, end, true /* throw if overflow */);

    return StringMemoryBuffer::CreateFromSwap(content);
  }


  bool FilesystemStorage::HasReadRange() const
  {
    return true;
  }


  uintmax_t FilesystemStorage::GetSize(const std::string& uuid) const
  {
    boost::filesystem::path path = GetPath(uuid);
    return boost::filesystem::file_size(path);
  }



  void FilesystemStorage::ListAllFiles(std::set<std::string>& result) const
  {
    namespace fs = boost::filesystem;

    result.clear();

    if (fs::exists(root_) && fs::is_directory(root_))
    {
      for (fs::recursive_directory_iterator current(root_), end; current != end ; ++current)
      {
        if (SystemToolbox::IsRegularFile(current->path().string()))
        {
          try
          {
            fs::path d = current->path();
            std::string uuid = ToString(d);
            if (Toolbox::IsUuid(uuid))
            {
              fs::path p0 = d.parent_path().parent_path().parent_path();
              std::string p1 = ToString(d.parent_path().parent_path());
              std::string p2 = ToString(d.parent_path());
              if (p1.length() == 2 &&
                  p2.length() == 2 &&
                  p1 == uuid.substr(0, 2) &&
                  p2 == uuid.substr(2, 2) &&
                  p0 == root_)
              {
                result.insert(uuid);
              }
            }
          }
          catch (fs::filesystem_error&)
          {
          }
        }
      }
    }
  }


  void FilesystemStorage::Clear()
  {
    namespace fs = boost::filesystem;
    typedef std::set<std::string> List;

    List result;
    ListAllFiles(result);

    for (List::const_iterator it = result.begin(); it != result.end(); ++it)
    {
      Remove(*it, FileContentType_Unknown /*ignored in this class*/);
    }
  }

  void FilesystemStorage::SetDbIndex(ServerIndex* severIndex) {
      _index = severIndex;
  }
  void FilesystemStorage::Remove(const std::string& uuid,
                                 FileContentType type)
  {
    LOG(INFO) << "Deleting attachment \"" << uuid << "\" of type " << static_cast<int>(type);

    namespace fs = boost::filesystem;

    fs::path p = GetPath(uuid);

    try
    {
      fs::remove(p);
    }
    catch (...)
    {
      // Ignore the error
    }

    // Remove the two parent directories, ignoring the error code if
    // these directories are not empty

    try
    {
#if BOOST_HAS_FILESYSTEM_V3 == 1
      boost::system::error_code err;
      fs::remove(p.parent_path(), err);
      fs::remove(p.parent_path().parent_path(), err);
#else
      fs::remove(p.parent_path());
      fs::remove(p.parent_path().parent_path());
#endif
    }
    catch (...)
    {
      // Ignore the error
    }
  }


  uintmax_t FilesystemStorage::GetCapacity() const
  {
    return boost::filesystem::space(root_).capacity;
  }

  uintmax_t FilesystemStorage::GetAvailableSpace() const
  {
    return boost::filesystem::space(root_).available;
  }


#if ORTHANC_BUILDING_FRAMEWORK_LIBRARY == 1
  FilesystemStorage::FilesystemStorage(std::string root) :
    fsyncOnWrite_(false)
  {
    Setup(root);
  }
#endif


#if ORTHANC_BUILDING_FRAMEWORK_LIBRARY == 1
  void FilesystemStorage::Read(std::string& content,
                               const std::string& uuid,
                               FileContentType type)
  {
    std::unique_ptr<IMemoryBuffer> buffer(Read(uuid, type));
    buffer->MoveToString(content);
  }
#endif
}

IStorageArea.h

添加class ServerIndex; 声明

/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2022 Osimis S.A., Belgium
 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this program. If not, see
 * <http://www.gnu.org/licenses/>.
 **/


#pragma once

#include "../IMemoryBuffer.h"
#include "../Enumerations.h"

#include <stdint.h>
#include <string>



namespace Orthanc
{
    class ServerIndex;
  class IStorageArea : public boost::noncopyable
  {
  public:
    virtual ~IStorageArea()
    {
    }

    virtual void Create(const std::string& uuid,
                        const void* content,
                        size_t size,
                        FileContentType type) = 0;

    virtual IMemoryBuffer* Read(const std::string& uuid,
                                FileContentType type) = 0;

    virtual IMemoryBuffer* ReadRange(const std::string& uuid,
                                     FileContentType type,
                                     uint64_t start /* inclusive */,
                                     uint64_t end /* exclusive */) = 0;

    virtual bool HasReadRange() const = 0;

    virtual void Remove(const std::string& uuid,
                        FileContentType type) = 0;


    virtual void SetDbIndex(ServerIndex *severIndex) = 0;


 

 
  };
}

MemoryStorageArea 类比修改

OrthancPlugins.cpp

class StorageAreaBase : public IStorageArea
    {
    private:
      OrthancPluginStorageCreate create_;
      OrthancPluginStorageRemove remove_;
      PluginsErrorDictionary&    errorDictionary_;
      ServerIndex* _index;
    protected:
      PluginsErrorDictionary& GetErrorDictionary() const
      {
        return errorDictionary_;
      }

      IMemoryBuffer* RangeFromWhole(const std::string& uuid,
                                    FileContentType type,
                                    uint64_t start /* inclusive */,
                                    uint64_t end /* exclusive */)
      {
        if (start > end)
        {
          throw OrthancException(ErrorCode_BadRange);
        }
        else if (start == end)
        {
          return new StringMemoryBuffer;  // Empty
        }
        else
        {
          std::unique_ptr<IMemoryBuffer> whole(Read(uuid, type));

          if (start == 0 &&
              end == whole->GetSize())
          {
            return whole.release();
          }
          else if (end > whole->GetSize())
          {
            throw OrthancException(ErrorCode_BadRange);
          }
          else
          {
            std::string range;
            range.resize(end - start);
            assert(!range.empty());
            
            memcpy(&range[0], reinterpret_cast<const char*>(whole->GetData()) + start, range.size());

            whole.reset(NULL);
            return StringMemoryBuffer::CreateFromSwap(range);
          }
        }
      }      
      
    public:
      StorageAreaBase(OrthancPluginStorageCreate create,
                      OrthancPluginStorageRemove remove,
                      PluginsErrorDictionary&  errorDictionary) : 
        create_(create),
        remove_(remove),
        errorDictionary_(errorDictionary)
      {
        if (create_ == NULL ||
            remove_ == NULL)
        {
          throw OrthancException(ErrorCode_Plugin, "Storage area plugin doesn't implement all the required primitives");
        }
      }

      virtual void Create(const std::string& uuid,
                          const void* content, 
                          size_t size,
                          FileContentType type) ORTHANC_OVERRIDE
      {
        OrthancPluginErrorCode error = create_
          (uuid.c_str(), content, size, Plugins::Convert(type));

        if (error != OrthancPluginErrorCode_Success)
        {
          errorDictionary_.LogError(error, true);
          throw OrthancException(static_cast<ErrorCode>(error));
        }
      }

      virtual void Remove(const std::string& uuid,
                          FileContentType type) ORTHANC_OVERRIDE
      {
        OrthancPluginErrorCode error = remove_
          (uuid.c_str(), Plugins::Convert(type));

        if (error != OrthancPluginErrorCode_Success)
        {
          errorDictionary_.LogError(error, true);
          throw OrthancException(static_cast<ErrorCode>(error));
        }
      }


      virtual void SetDbIndex(ServerIndex* severIndex) ORTHANC_OVERRIDE {
          _index = severIndex;
      }
    };

OrthancInitialization.cpp

  namespace
  {
    // Anonymous namespace to avoid clashes between compilation modules

    class FilesystemStorageWithoutDicom : public IStorageArea
    {
    private:
      FilesystemStorage storage_;
      ServerIndex* _index;
    public:
      FilesystemStorageWithoutDicom(const std::string& path,
                                    bool fsyncOnWrite) :
        storage_(path, fsyncOnWrite)
      {
      }

      virtual void Create(const std::string& uuid,
                          const void* content, 
                          size_t size,
                          FileContentType type) ORTHANC_OVERRIDE
      {
        if (type != FileContentType_Dicom)
        {
          storage_.Create(uuid, content, size, type);
        }
      }

      virtual IMemoryBuffer* Read(const std::string& uuid,
                                  FileContentType type) ORTHANC_OVERRIDE
      {
        if (type != FileContentType_Dicom)
        {
          return storage_.Read(uuid, type);
        }
        else
        {
          throw OrthancException(ErrorCode_UnknownResource);
        }
      }

      virtual IMemoryBuffer* ReadRange(const std::string& uuid,
                                       FileContentType type,
                                       uint64_t start /* inclusive */,
                                       uint64_t end /* exclusive */) ORTHANC_OVERRIDE
      {
        if (type != FileContentType_Dicom)
        {
          return storage_.ReadRange(uuid, type, start, end);
        }
        else
        {
          throw OrthancException(ErrorCode_UnknownResource);
        }
      }

      virtual bool HasReadRange() const ORTHANC_OVERRIDE
      {
        return storage_.HasReadRange();
      }

      virtual void Remove(const std::string& uuid,
                          FileContentType type) ORTHANC_OVERRIDE
      {
        if (type != FileContentType_Dicom)
        {
          storage_.Remove(uuid, type);
        }
      }

      virtual void SetDbIndex(ServerIndex* severIndex) ORTHANC_OVERRIDE {
          _index = severIndex;
      }
    };
  }